In order to obtain highly precise and stable magnetic signal, a geomagnetic signal acquisition and storage system based on magnetic resistance sensor was designed and parameter models about three-axis magnetic resistance sensor sensitivity errors, non-orthogonal error and zero drift error were established. An objective optimization function about error parameters with engineering optimization design thought was established. The coordinate transformation method was adopted to obtain optimal error compensation parameters. The optimal error compensation parameters were used to make standard deviation is reduced from 0.03 Gs to 0.01 Gs through simulation. Simulation results show that the precision and stability of the magnetic data can be effectively raised by error compensation for the actual magnetic data.